keyvalue

Format

cg keyvalue ?options? ?infile? ?outfile?

Summary

Converts data in tsv format from wide format (data for each sample in separate columns) to keyvalue format.

Description

Converts a tsv file containing different values of an object in one row (different fields) into a key-value format: Each of the rows is split into multiple rows (one for each data column) containing fields identifying the object followed by the fields key (fieldname of data column in original) \ and value (value in the data column).

The fields identifying the object can be specified using the -idfields option, but defaults to sample or id. sample as id field is treated special (unless an actual sample field is present in the file): The actual sample value is extracted from the fieldname (field-sample).

Arguments

infile: file to be converted, if not given, uses stdin. File may be compressed.
outfile: write results to outfile, if not given, uses stdout

Options

-idfields list: which fields identify the object (default sample or id)
-samplefields samplefields: Using this option, sample names that consist of several parts separated by - (as typical in genomecomb output, e.g. -gatk-rdsbwa-sample1) are split up in separate fields with the field names given by samplefields
-keyname keyname: change the fieldname of the column containing the keys from the default "key" to keyname
-valuename valuename: change the fieldname of the column containing the values from the default "value" to valuename

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